A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-07-26, 16:23 IDT
based on data in:
/lustre1/home/mass/amalia/montipora_mapping/outputs/multiqc_input
General Statistics
| Sample Name | % Aligned |
|---|---|
| SRR14864064_hisat2 | 63.4% |
| SRR14864065_hisat2 | 65.0% |
| SRR14864066_hisat2 | 47.3% |
| SRR14864067_hisat2 | 73.0% |
| SRR14864068_hisat2 | 71.9% |
| SRR14864069_hisat2 | 79.9% |
| SRR14864070_hisat2 | 82.1% |
| SRR14864071_hisat2 | 80.8% |
| SRR14864072_hisat2 | 73.0% |
Bowtie 2 / HiSAT2
Bowtie 2 and HISAT2 are fast and memory-efficient tools for aligning sequencing reads against a reference genome. Unfortunately both tools have identical log output by default, so it is impossible to distiguish which tool was used. .DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4.
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.